BIOL2056 Lecture 20: Model Systems in Cell Biology PDF

BIOL2056: Lectures 20 Model systems to study Cell Biology 17 From cells to tissue: ECM 18 From cells to tissue: Cell Adhesion & communication 19 From cells to tissue: Cell Adhesion & communication 20 Model systems to study Cell Biology Dr Nicole Prior...

BIOL2056: Lectures 20 Model systems to study Cell Biology 17 From cells to tissue: ECM 18 From cells to tissue: Cell Adhesion & communication 19 From cells to tissue: Cell Adhesion & communication 20 Model systems to study Cell Biology Dr Nicole Prior [email protected]  Learning outcomes: Lecture 20 Model systems By the end of this session you should be able to: Explain why researchers use models Describe different types of models systems with advantages & limitations of each Single-cell Multicellular Mammalian systems Computational models Describe the purpose of commonly used experimental techniques What is a model and why do we use them? A simplified/convenient version of a complex entity. The model captures key characteristics of the entity needed to address the task at hand. It is not possible/ethical to study what we want directly (e.g. human disease) Model organisms are non-human species – used to help understand biological processes Single cell organisms - E.coli (Escherichia coli) Fast growth in chemically defined media Relatively cheap culture media Several molecular tools for manipulation Extensive knowledge of its genetics and genomics Extensive knowledge on its transcriptome, proteome, and metabolome Several strains are considered biosafety level 1 (K12) Disadvantage – doesn’t have a nucleus/chromatin, not all protein modification mechanisms e.g. glycosylation  Single cell organisms - Yeast Simple eukaryotic organism – many essential cellular processes are the same in yeast and humans. S. pombe resembles animal cells in terms of (division pattern; centromeres; introns; heterochromatin) S. cerevisiae is more similar to animal cells in terms of (relative lengths of G1 and G2; synaptonemal complexes). Rapid growth (1.5 or 2.5 hours) Non-pathogenic Efficient transformation by exogenous DNA Efficient homologous recombination Simple genetic screens Mammalian systems - Mouse (Mus musculus) The mouse is closely related to humans with a striking similarity to us in terms of anatomy, physiology and genetics. The time between a mouse being born and giving birth (generation time) is short, usually around 10 weeks. This means several generations can be observed at once. Amenable for genetic manipulation -Many knock out, knock in and conditional expression lines exist  Mammalian systems – Cell culture Cells isolated from a system and grown in vitro Cheaper to study cells in culture than a whole organism Can do more perturbation and measurements Most cell lines are transformed -loose some properties compared to normal cells in vivo – can lead to artefacts  Recent advances - organoids ECM Organoids  in vitro 3D cellular cluster  derived from stem cells ESCs, iPSCs or tissue resident stem cells  self-renewal  self-organization Nguyen & McAleavey,  How do you grow an organoid? Organoids can be initiated from three main types of stem cells: Modulating cell signalling is key Lancaster et al., Science, 2014 2009 – mouse intestinal organoids Distinct crypt-like and villus- like domains border a central lumen containing dead cells extruded from the constantly renewing epithelial layer. Sato et al., Nature, 2009 2013 – human brain organoids Lancaster et al., Nature, 2013  2017 – human brain organoids Neurons in the cerebral organoids exhibit action potentials and spontaneous ensemble activities. Watanabe et al., Cell Reports, 2017 2015 – human cardiac organoids Ma et al., Nature Communications, 2015 Organoids represent an important bridge between traditional 2D cultures and in vivo models;  more physiologically relevant than monolayer culture models.  far more amenable to manipulation of niche components, signalling pathways and genome editing compared to in vivo models.  Drug efficacy testing / Drug safety testing  Disease modelling  Regenerative medicine  As model systems for basic research - In particular for human biology A simplified view of cell biology Different levels need different detection methods. At the transcriptional level, mRNA can be measured by; In situ hybridisation qPCR  At the translational level, proteins can be detected using; SDS PAGE + Immunochemistry ELISA Coomassie (A) / Wetsern Blot (B)  A simplified view of cell biology Whole genome sequencingRNA sequencing Mass Spectrometry  Lecture Summary There are different types of models systems each with their specific advantages & limitations Recent advances have generated new types of models to study cell biology - organoids When designing an experiment it is important to consider what you need to measure and what techniques you may use